The Modified format was introduced in 2001. Tournaments in the 2001-2002 season were played in a format that only allowed cards from the Team Rocket set on up through Neo Genesis (with the exception of Sneasel, which was banned). Since then, Play! Pokémon has continued to rotate sets approximately once per year, usually after the World Championships, to keep the game fresh and, some speculate, to keep players buying cards. The 2009-2010 tournament season did not feature a rotation, and the rotation for the 2010-2011 season rotated out only four sets, keeping roughly two years' worth of cards in the pool.

If a card in a Modified-legal expansion is a reprint of an older card, all prints of the card can be played in a Modified-legal deck (i.e. Base SetPotion, recently reprinted in Black & White). However, some cards significantly differ in wording between older prints and newer prints (i.e. Charizard from the Base Set compared to its Stormfront iteration); those cards require a reference outside the deck in order to use the older prints in a Modified-legal deck. A reference must be either a new version of the card or a printout of the card's entry from the official Card-Dex.

Prior to the 2009-2010 tournament season, foreign-language prints of cards could also be played without limit, as long as the user provided a local-language reference outside the deck. Starting with the 2009-2010 season, however, sanctioned events began to require players to play with cards printed in English or an area's local language (for example: players in the United States are restricted to English cards only, whereas players in Canada can also use cards in French). This caused an outcry in the TCG community. Many American players had invested heavily in Japanese cards, which were generally less expensive, to use in tournaments. As a result, the rules were amended for the 2009-2010 tournament season to allow up to 10% of a player's deck (six cards) to consist of foreign-language cards. Beginning in the 2010-2011 season, Play! Pokémon followed through with their initial plan to allow only English and local-language cards in premier events.